COPD is the fourth-leading cause of death in the United States, and cigarette smoking has been proven to be the most important environmental contributor. DNA methylation varies with aging and with environmental exposures such as cigarette smoking, and is a critical mediator of gene expression. Additionally, there are data to suggest that DNA methylation patterns are influenced by DNA polymorphisms. Although widely studied in cancers, including lung cancer, the wide-scale investigation of variable methylation in COPD and the correlation with polymorphisms and gene expression have not been comprehensively performed. COPD has both local pulmonary and systemic manifestations, all of which are likely impacted by a combination of genetic, genomic and epigenetic pathways. We hypothesize that characterization of genome-wide DNA methylation marks will provide important scientific insights into COPD. We also hypothesize that characterizing genome-wide DNA methylation marks correlated with IREB2, HHIP and FAM13A variants may provide important insights into regulation of these three COPD candidate genes. To address these two hypotheses, the broad goals of this project include: 1) to identify methylation signatures that discriminate COPD susceptibility and COPD severity and 2) to use comparative epigenetic to identify methylation marks that are altered by cigarette smoke exposure and likely impact the development of COPD and its component processes, emphysema and airway disease. In this project, genome-wide methylation patterns will be characterized for lung tissue and blood DNA from human subjects in our Lung Tissue Population. Methylation patterns will also be characterized for murine lung DNA after in vivo exposure of wild-type C57BL/6 {susceptible) and NZW/LacJ (resistant) mice to cigarette smoke. We will use statistical modeling and comparative epigenetics to select COPD gene candidates to replicate using pyrosequencing methods in the Bronchoscopy Population, a second human cohort. This project will characterize DNA methylation marks important to COPD and will assess the epigenetic impact of variation in IREB2, HHIP and FAM13A as key COPD candidate genes. We will use comparative, translational and integrative genetics, genomics and epigenomics to identify functional features of COPD susceptibility genes. We expect methylation marks with replicated associations will provide novel insights into the pathobiology of COPD and the genetic context that influences the epigenomic impact of cigarette smoking. Lastly, we will integrate SNP variation, methylation marks and gene expression data to define the most comprehensive causal model of COPD.